ETC5521 Assignment 1
Measles Vaccination
Aryan Jain
Emily Sheehan
Jimmy Effendy
DIYAO CHEN
2020-09-17
This assignment is for ETC5521 Assignment 1 by Team Lorikeet comprising of Aryan Jain, Emily Sheehan, Jimmy Effendy, and DIYAO CHEN.
1 Introduction and Motivation
Measles is a highly infectious disease caused by the Measles virus. It can lead to pneumonia, infections of the middle ear, swelling of the brain and death.
A vaccine exists to prevent the onset of measles as there is no treatment. The vaccine involves the injection of attenuated measles antigens that stimulate the production of antibodies and memory cells, providing long-term protection against the virus. When administered properly, the vaccine is 90.5% effective within 72 hours of exposure (Barrabeig et al., 2011).
Unfortunately there is a growing number of individuals refusing vaccination, particularly in the US (Phadke et al., 2016). In Texas, the number of unvaccinated children attaining exemptions to attend school has increased by 28 times since 2003 (Sinclair et al., 2019). This has led to several outbreaks of vaccine preventable diseases, such as Measles. If this trend continues, there could be calamitous consequences.
This paper hopes to determine whether there is a relationship between socioeconomic status and MMR vaccination rate. Specifically, it explores how MMR vaccination rates fluctuate across different school types, states, income levels, enrollment numbers, educational attainment level, and proportion of foregin born populations. It will also compare the MMR vaccination rates against the overall vaccination rates.
Specifically, this paper hopes to answer the following questions:
Primary Question:
- Does Measles vaccination rate improve with better socioeconomic conditions?
Secondary Questions:
- Are the MMR vaccination rates higher in private schools?
- How does school’s MMR Vaccination rate compare to the school’s overall vaccination rate?
- Which states have the highest vaccination rates?
- Are MMR Vaccination rates higher in higher income counties?
- What does number of enrollment tell us about MMR vaccination rates?
- Are MMR vaccination rates lower in areas with higher proportion of foreign-born population?
First, the paper will discuss the data used and how it is prepared for the analysis. Then, analysis and findings about the research questions will be presented and discussed.
2 Data Description
To analyse the relationship a dataset was retrieved from Wall Street Journal (WSJ). The data comprises of vaccination rates for 46,412 schools in 32 U.S states and was retrieved from The Wall Street Journal. The variables include; the school academic year, the school’s state, city, county, district, name, type, enrollment, MMR (measles, mumps and rubella) vaccination rate, overall vaccination rate, latitude, longitude and the percentage of students exempted from vaccinations due to personal, religious or medical reasons. The state health departments provided the vaccination data and the National Center for Education Statistic’s provided the school location, which was matched against the school name. In the case that there was no match, the school’s location was found with Google Maps API.
Additional data from the U.S. Census Bureau is also retrieved for 2018 county level income per capita, educational attainment level, and the number of foreign-born population. This was done by utilizing Census data API provided by the Census Bureau as well as with tidycensus package.
2.1 Data Limitation
One of the limitation of the WSJ measles data is that there is inconsistencies in data collection methods. The data was collected in the 2017-18 school year for 11 states, but for the remaining 21 states, it was collected in 2018-19 school year. Moreover, with the help of naniar package, it can be easily identified that this dataset has a considerable amount of missing values. Although every precaution has been taken to ensure accurate figures have been calculated, some of the MMR rates, overall vaccination rates and school types were missing from the original dataset. The following variables are largely unusable as due to its high number of missing values:
xrel: the percentage of students exempted from vaccinations due to personal reasonsxmed: the percentage of students exempted from vaccinations due to medical reasonsxper: the percentage of students exempted from vaccinations due to religious reasonsdistrict: school district
2.2 Data Cleaning and Transformation
The individual state dataset was scraped from the Tidy Tuesday Github repository and combined with the existing measles dataset with left_join to extract the longitude and latitude variables from it. Various functions from the rvest package were used to scrape the data including read_html and html_table.
A considerable amount of data wrangling needed to be done for the U.S. census dataset as they do not provide descriptions of what each variable represents (e.g. variable B19301_001 represents Income Per Capita). In addition variable county_state, comprising of county and state, needed to be added for the measle and U.S. census dataset. This variable is used as a key to merge the measles and U.S. census dataset. This is achieved by utilizing tidyverse and janitor packages.
3 Analysis and Findings
3.1 Are the MMR Vaccination Rates Higher in Private Schools?
The measles data was filtered to remove missing school type, overall vaccination rate and MMR rate. It was grouped by type of school and the average MMR vaccination rate and overall vaccination rate was calculated using the mean function. The tibble generated was named school_type_average. Then, the average MMR rates from the school_type_average tibble were plotted. The rates were annotated accordingly, to draw attention to the difference between the MMR vaccination rate for each school type.
| Type | Average MMR Vaccination Rate (%) |
|---|---|
| BOCES | 98.75 |
| Public | 96.16 |
| Nonpublic | 94.38 |
| Kindergarten | 94.21 |
| Private | 93.32 |
| Charter | 87.96 |
Figure 3.1: Box plot of School’s MMR Vaccination Rates by School Types
The MMR vaccination rate was the highest in public schools, as seen in the table above. This is consistent with findings from a study conducted by Shaw (2014) where it was found that private schools have higher rates of exemptions for immunisations than public schools.
3.2 How Does School’s MMR Vaccination Rate Compare to the School’s Overall Vaccination Rate?
| School Type | School MMR Vaccination Rate (%) | School Overall Vaccination Rate (%) | Rate Differences (%) |
|---|---|---|---|
| Kindergarten | 94.20 | 87.99 | 6.21 |
| Private | 93.16 | 91.37 | 1.78 |
| Public | 95.90 | 94.51 | 1.38 |
The school_type_average data was tabulated to compare the overall vaccination rate and MMR vaccination rate. Then, both rates were plotted according to school type.
When comparing the vaccination rates according to school type, it is clear that the overall vaccination rate is lower than the MMR vaccination rate for all school types as seen in the plot below. Public schools have the highest overall vaccination rate and MMR rate.
3.3 Which states have lowest vaccination rates?
The measles data was grouped by state and then the average MMR and overall vaccination rate were calculated. Then, the map_data function was used to create a tibble containing the geographical information of each state. This data was merged with the measles_states data, which contains the average MMR and overall vaccination rate for each state. Any missing data or negative values were removed and the remaining data was plotted onto a map and bar chart using geom_polygon and geom_col, respectively. The ggplotly function was used to make the maps interactive.
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## - attr(*, "validate")= logi TRUEThe state with the highest MMR vaccination rate is Illinois at 97.39% and the state with the lowest MMR vaccination rate is Massachusetts at 57.68% as shown in the figure below.
The state with the highest overall vaccination rate is North Caroline at 96.779%, while the state with the lowest vaccination rate is Washington at 75.238% as shown in the figure above. It is difficult to compare the individual states MMR vaccination rate with the overall vaccination rate due to the missing data. However, California, Vermont, Ohio and Oregon have similar MMR and overall vaccination rates.
3.4 Are MMR Vaccination Rates Lower in Lower Income Counties?
To analyse the average income of the states with the highest and lowest vaccination rate, an external dataset from Tax Foundation:Github Repository was retrieved. This data was merged with the measles data grouped by state, and the top and bottom five observations were tabulated for both the vaccination rates. The vaccination rate and income data were plotted using geom_col and gg_arrange, and ordered in descending order.
| States | MMR Vaccination Rate (%) | Per Capita Income |
|---|---|---|
| Illinois | 97.62 | $28,105.72 |
| Connecticut | 96.49 | $41,021.25 |
| Massachusetts | 96.26 | $40,222.43 |
| South Dakota | 95.25 | $28,617.14 |
| Vermont | 95.19 | $31,966.00 |
| States | MMR Vaccination Rate (%) | Per Capita Income |
|---|---|---|
| Washington | 88.14 | $29,274.29 |
| Minnesota | 90.89 | $30,827.47 |
| Arizona | 91.38 | $23,459.40 |
| Maine | 92.24 | $28,983.25 |
| Texas | 92.32 | $27,504.22 |
The states with the highest MMR vaccination rate were; Illinois, Pennsylvania, Utah, Colorado and New York. These states each have an average per capita income of $56,839, $56,225, $46,320, $58,456 and $68,668, respectively, as shown in the plot below.
3.5 What Does Enrollment Numbers Tell Us about MMR Vaccination Rates?
| County | State | MMR Vaccination Rates (%) | Enrollment |
|---|---|---|---|
| Jackson | Colorado | 20.00 | 10 |
| Mille Lacs | Minnesota | 66.52 | 52 |
| Nicollet | Minnesota | 67.83 | 16 |
| Aitkin | Minnesota | 67.89 | 57 |
| Pennington | Minnesota | 69.59 | 49 |
3.6 Are MMR Vaccination Rates Lower in Areas with Higher Proportion of Foreign Born Population?
3.7 Education
4 Conclusion
The analysis has revealed that it is likely that there is no association with socioeconomic status and vaccination rates. Private schools, which are more expensive than public schools thus inferring greater socioeconomic status, have a lower average MMR and average overall vaccination rate than their public counterparts. The two states with the lowest MMR vaccination rate; Connecticut and Massachusetts, had the two highest average per capita incomes. Similarly, Washington had the lowest overall vaccination rate and one of the highest average per capita incomes. Therefore, it is unlikely that vaccination rate improves with socioeconomic status.
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